54797-48-7Relevant academic research and scientific papers
Catalytic properties of 2,3-dihydroxybiphenyl 1,2-dioxygenase from Dyella Ginsengisoli LA-4 immobilized on mesoporous silica SBA-15
Qu, Yuanyuan,Kong, Chunlei,Zhou, Hao,Shen,Wang, Jingwei,Shen, Wenli,Zhang, Xuwang,Zhang, Zhaojing,Ma, Qiao,Zhou, Jiti
, p. 136 - 142 (2014)
In this study, 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) from Dyella ginsengisoli LA-4 was immobilized on the mesoporous silica SBA-15 in order to improve its stability with relatively high retaining activities. By Fourier transformed infrared spectros
Identification of an acyl-enzyme intermediate in a meta-cleavage product hydrolase reveals the versatility of the catalytic triad
Ruzzini, Antonio C.,Ghosh, Subhangi,Horsman, Geoff P.,Foster, Leonard J.,Bolin, Jeffrey T.,Eltis, Lindsay D.
body text, p. 4615 - 4624 (2012/04/23)
Meta-cleavage product (MCP) hydrolases are members of the α/β-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 A resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of 18O into the benzoate produced during hydrolysis in H218O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ESred, previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.
The catalytic serine of meta-cleavage product hydrolases is activated differently for C-O bond cleavage than for C-C bond cleavage
Ruzzini, Antonio C.,Horsman, Geoff P.,Eltis, Lindsay D.
experimental part, p. 5831 - 5840 (2012/09/22)
meta-Cleavage product (MCP) hydrolases catalyze C-C bond fission in the aerobic catabolism of aromatic compounds by bacteria. These enzymes utilize a Ser-His-Asp triad to catalyze hydrolysis via an acyl-enzyme intermediate. BphD, which catalyzes the hydrolysis of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) in biphenyl degradation, catalyzed the hydrolysis of an ester analogue, p-nitrophenyl benzoate (pNPB), with a kcat value (6.3 ± 0.5 s-1) similar to that of HOPDA (6.5 ± 0.5 s-1). Consistent with the breakdown of a shared intermediate, product analyses revealed that BphD catalyzed the methanolysis of both HOPDA and pNPB, partitioning the products to benzoic acid and methyl benzoate in similar ratios. Turnover of HOPDA was accelerated up to 4-fold in the presence of short, primary alcohols (methanol > ethanol > n-propanol), suggesting that deacylation is rate-limiting during catalysis. In the steady-state hydrolysis of HOPDA, kcat/Km values were independent of methanol concentration, while both kcat and Km values increased with methanol concentration. This result was consistent with a simple model of nucleophilic catalysis. Although the enzyme could not be saturated with pNPB at methanol concentrations of >250 mM, kobs values from the steady-state turnover of pNPB at low methanol concentrations were also consistent with a nucleophilic mechanism of catalysis. Finally, transient-state kinetic analysis of pNPB hydrolysis by BphD variants established that substitution of the catalytic His reduced the rate of acylation by more than 3 orders of magnitude. This suggests that for pNPB hydrolysis, the serine nucleophile is activated by the His-Asp dyad. In contrast, rapid acylation of the H265Q variant during C-C bond cleavage suggests that the serinate forms via a substrate-assisted mechanism. Overall, the data indicate that ester hydrolysis proceeds via the same acyl-enzyme intermediate as that of the physiological substrate but that the serine nucleophile is activated via a different mechanism.
Characterization of a transcriptional regulatory gene involved in dibenzofuran degradation by nocardioides sp. strain DF412
Sukda, Parichat,Gouda, Nao,Ito, Emi,Miyauchi, Keisuke,Masai, Eiji,Fukuda, Masao
body text, p. 508 - 516 (2010/04/29)
Nocardioides sp. DF412 degrades dibenzofuran (DF) to salicylate through the sequential actions of DF dioxygenase (dfdA), extradiol dioxygenase (dfdB), and hydrolase (dfdC). The involvement of a TetR-type regulator gene dfdS in the dfdB and dfdS gene expre
Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans Strain CA10
Nojiri, Hideaki,Taira, Hiroko,Iwata, Kenichi,Morii, Kenichi,Nam, Jeong-Won,Yoshida, Takako,Habe, Hiroshi,Nakamura, Shugo,Shimizu, Kentaro,Yamane, Hisakazu,Omori, Toshio
, p. 36 - 45 (2007/10/03)
2-Hydroxy-6-oxo-6-(2′-aminophenyl)-hexa-2,4-dienoic acid [6-(2′-aminophenyl)-HODA] hydrolase, involved in carbazole degradation by Pseudomonas resinovorans strain CA10, was purified to near homogeneity from an overexpressing Escherichia coli strain. The enzyme was dimeric, and its optimum pH was 7.0-7.5. Phylogenetic analysis showed the close relationship of this enzyme to other hydrolases involved in the degradation of monocyclic aromatic compounds, and this enzyme was specific for 2-hydroxy-6-oxo-6-phenylhexa-2,4- dienoic acid (6-phenyl-HODA), having little activity toward 2-hydroxy-6- oxohepta-2,4-dienoic acid and 2-hydroxymuconic semialdehyde. The enzyme had a Km of 2.51 μM and kcat of 2.14 (s-1) for 6-phenyl-HODA (50 mM sodium phosphate, pH 7.5, 25°C). The effect of the presence of an amino group or hydroxyl group at the 2′-position of phenyl moiety of 6-phenyl-HODA on the enzyme activity was found to be small; the activity decreased only in the order of 6-(2′-aminophenyl)-HODA (2.44 U/mg) > 6-phenyl-HODA (1.99 U / mg) > 2-hydroxy-6-oxo-6-(2′- hydroxyphenyl)-hexa-2,4-dienoic acid (1.05 U/mg). The effects of 2′-substitution on the activity were in accordance with the predicted reactivity based on the calculated lowest unoccupied molecular orbital energy for these substrates.
Purification and Some Properties of 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid(HOPDA) Reducing Enzyme from Pseudomonas cruciviae S93B1 Involved in the Degradation of Biphenyl
Omori, Toshio,Ishigooka, Hiroshi,Minoda, Yasuji
, p. 1513 - 1518 (2007/10/02)
Pseudomonas cruciviae S93B1 produced three HOPDA reducing enzymes (I, II, III), found by chromatography on DEAE-Sepharose CL-6B.The purified HOPDA reducing enzyme III was homogeneous on polyacrylamide gel and has a mol. wt. of about 170,000 by Sephadex G-
